[English] 日本語
Yorodumi
- PDB-4itv: Structure of a 16 nm protein cage designed by fusing symmetric ol... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4itv
TitleStructure of a 16 nm protein cage designed by fusing symmetric oligomeric domains, triple mutant, P212121 form
ComponentsNon-haem bromoperoxidase BPO-A2, Matrix protein 1
KeywordsOXIDOREDUCTASE / protein design / bionanotechnology / protein assembly / symmetric oligomeric domains / biomaterials
Function / homology
Function and homology information


Assembly of Viral Components at the Budding Site / Influenza Infection / Fusion of the Influenza Virion to the Host Cell Endosome / Release / Budding / Packaging of Eight RNA Segments / Uncoating of the Influenza Virion / Entry of Influenza Virion into Host Cell via Endocytosis / Viral RNP Complexes in the Host Cell Nucleus / NEP/NS2 Interacts with the Cellular Export Machinery ...Assembly of Viral Components at the Budding Site / Influenza Infection / Fusion of the Influenza Virion to the Host Cell Endosome / Release / Budding / Packaging of Eight RNA Segments / Uncoating of the Influenza Virion / Entry of Influenza Virion into Host Cell via Endocytosis / Viral RNP Complexes in the Host Cell Nucleus / NEP/NS2 Interacts with the Cellular Export Machinery / Viral mRNA Translation / antibiotic biosynthetic process / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / viral budding from plasma membrane / peroxidase activity / structural constituent of virion / host cell nucleus / virion membrane / RNA binding / extracellular region / plasma membrane
Similarity search - Function
Influenza matrix M1, N-terminal subdomain 1 / Influenza matrix protein M1, N-terminal subdomain 2 / Influenza Virus Matrix Protein; Chain A, domain 1 / Matrix protein 1 / Influenza matrix M1, N-terminal / Influenza matrix M1, C-terminal / Influenza matrix M1, N-terminal subdomain 1 / Influenza matrix M1, N-terminal subdomain 2 / Influenza virus matrix protein M1 / Influenza Matrix protein (M1) ...Influenza matrix M1, N-terminal subdomain 1 / Influenza matrix protein M1, N-terminal subdomain 2 / Influenza Virus Matrix Protein; Chain A, domain 1 / Matrix protein 1 / Influenza matrix M1, N-terminal / Influenza matrix M1, C-terminal / Influenza matrix M1, N-terminal subdomain 1 / Influenza matrix M1, N-terminal subdomain 2 / Influenza virus matrix protein M1 / Influenza Matrix protein (M1) / Influenza Matrix protein (M1) C-terminal domain / Influenza Matrix protein (M1) C-terminal domain / Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Arc Repressor Mutant, subunit A / Up-down Bundle / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Matrix protein 1 / Non-haem bromoperoxidase BPO-A2
Similarity search - Component
Biological speciesStreptomyces aureofaciens (bacteria)
Influenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.598 Å
AuthorsLai, Y.-T. / Sawaya, M.R. / Yeates, T.O.
CitationJournal: J.Am.Chem.Soc. / Year: 2013
Title: Structure and flexibility of nanoscale protein cages designed by symmetric self-assembly.
Authors: Lai, Y.T. / Tsai, K.L. / Sawaya, M.R. / Asturias, F.J. / Yeates, T.O.
History
DepositionJan 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.2Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Non-haem bromoperoxidase BPO-A2, Matrix protein 1
B: Non-haem bromoperoxidase BPO-A2, Matrix protein 1
C: Non-haem bromoperoxidase BPO-A2, Matrix protein 1
D: Non-haem bromoperoxidase BPO-A2, Matrix protein 1
E: Non-haem bromoperoxidase BPO-A2, Matrix protein 1
F: Non-haem bromoperoxidase BPO-A2, Matrix protein 1
G: Non-haem bromoperoxidase BPO-A2, Matrix protein 1
H: Non-haem bromoperoxidase BPO-A2, Matrix protein 1
I: Non-haem bromoperoxidase BPO-A2, Matrix protein 1
J: Non-haem bromoperoxidase BPO-A2, Matrix protein 1
K: Non-haem bromoperoxidase BPO-A2, Matrix protein 1
L: Non-haem bromoperoxidase BPO-A2, Matrix protein 1


Theoretical massNumber of molelcules
Total (without water)603,37612
Polymers603,37612
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35620 Å2
ΔGint-97 kcal/mol
Surface area187760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.620, 156.610, 321.150
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Non-haem bromoperoxidase BPO-A2, Matrix protein 1 / BPO2 / Bromide peroxidase / M1


Mass: 50281.359 Da / Num. of mol.: 12 / Mutation: K118A, L279Q, Q24T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces aureofaciens (bacteria), (gene. exp.) Influenza A virus
Strain: A/Puerto Rico/8/1934 H1N1 / Gene: bpoA2, BROMOPEROXIDASE A2 and M1 Matrix, M / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P29715, UniProt: P03485, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: 0.1M Na Citrate pH 4.4, 10% PEG 3000, vapor diffusion, hanging drop, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 26, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.598→160.575 Å / Num. all: 76475 / Num. obs: 76475 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 102.21 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 16.61
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
3.6-3.690.6192.5247395452195.7
3.69-3.790.4553.4251445470199.1
3.79-3.90.3494.37240725315198.7
3.9-4.020.2835.43227725155198.2
4.02-4.160.2166.63198574852195.7
4.16-4.30.1738.7234174900199.7
4.3-4.460.12811.31228084759199.7
4.46-4.650.11212.71217244576199.7
4.65-4.850.09414.91205514358199.6
4.85-5.090.08316.26197004204199.4
5.09-5.360.07916.86182953992199.3
5.36-5.690.07218.35169303783199
5.69-6.080.06917.9139103388195.1
6.08-6.570.05921.73152123324198.6
6.57-7.20.04328.33145233063199.4
7.2-8.050.03138.38128642779199.1
8.05-9.290.02252.23112882486199
9.29-11.380.0257.2587522068196.6
11.38-16.090.01960.1968631591194.5
16.09-160.5750.0262.514152960196.8

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.6 Å96.14 Å
Translation3.6 Å96.14 Å

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.1phasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BRO and 1AA7

1bro

1aa7


Resolution: 3.598→96.14 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8376 / SU ML: 0.39 / σ(F): 1.99 / Phase error: 23.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2402 3821 5 %random
Rwork0.2061 ---
all0.2078 76445 --
obs0.2078 76445 98.28 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 423.59 Å2 / Biso mean: 151.8637 Å2 / Biso min: 53.78 Å2
Refinement stepCycle: LAST / Resolution: 3.598→96.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms40776 0 0 0 40776
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00341700
X-RAY DIFFRACTIONf_angle_d0.60956748
X-RAY DIFFRACTIONf_chiral_restr0.0426408
X-RAY DIFFRACTIONf_plane_restr0.0047392
X-RAY DIFFRACTIONf_dihedral_angle_d13.19214808
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.5984-3.64390.3171320.30072508264092
3.6439-3.69190.28431400.28512672281299
3.6919-3.74250.34561410.27032676281799
3.7425-3.79590.25571410.25962672281399
3.7959-3.85260.2971400.24952655279599
3.8526-3.91280.27121400.24212668280899
3.9128-3.9770.28961410.23832676281798
3.977-4.04550.27041380.24452629276798
4.0455-4.11910.24831370.22422590272795
4.1191-4.19830.24251380.22092635277398
4.1983-4.2840.24431420.204527152857100
4.284-4.37720.22481430.19727202863100
4.3772-4.4790.2491420.19626952837100
4.479-4.5910.25281420.199726992841100
4.591-4.71510.21921450.200327402885100
4.7151-4.85390.24291410.18726932834100
4.8539-5.01050.22191440.182327212865100
5.0105-5.18960.22711420.1882699284199
5.1896-5.39740.24711430.19442721286499
5.3974-5.6430.21521420.18772700284299
5.643-5.94050.26811400.21632662280297
5.9405-6.31260.26911390.22562635277495
6.3126-6.79990.2651450.218427622907100
6.7999-7.48390.22191450.19682746289199
7.4839-8.56630.21121450.17962759290499
8.5663-10.79030.18581460.14972770291698
10.7903-96.1740.23721470.22572806295395
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.17710.22960.90683.0007-1.01124.29350.065-0.0024-0.10970.34220.03820.2248-0.1449-0.2475-0.10150.47040.01740.09850.6516-0.14120.530416.657447.4243342.8757
29.6883-3.44784.37677.2286-2.14276.90350.264-0.43470.23590.0561-0.5666-0.22280.16710.3730.29950.7864-0.01110.03031.0670.11720.4977-13.529739.8594371.1818
33.26550.52320.63223.82130.88862.896-0.26030.62810.4601-0.8909-0.01660.202-0.7725-0.04520.26940.99350.0191-0.09760.78360.02390.58214.728567.675311.3918
48.46754.9857-4.34625.7022-3.68928.2636-0.17190.01810.1989-0.2130.0025-0.0665-0.55290.20170.11421.08620.1717-0.12820.6077-0.08560.57821.387588.8284346.7508
53.0607-0.73121.28443.2909-0.04734.41020.06570.0836-0.2959-0.2435-0.13530.96710.1328-0.81420.06060.5009-0.0106-0.06880.9934-0.18231.015-9.831840.1002317.4054
69.7289-4.6225-0.17862.7352-0.23997.53780.10610.17431.29480.1158-0.1491-0.9076-1.75720.26570.05961.2248-0.1065-0.0340.9882-0.01721.7462-38.920166.5276304.3239
73.1089-0.1242-0.63663.6498-0.12242.71170.0122-0.19510.7969-1.0602-0.16440.1721-0.606-0.4290.11311.30550.2179-0.2820.8139-0.28340.939414.7307111.5375372.5944
84.33723.3062-0.76632.1299-1.81696.10020.1487-0.0020.6622-0.61740.35471.34940.067-0.9529-0.65921.72470.4509-0.39321.5004-0.02661.8437-19.2818118.429350.517
92.6372-0.1882-0.31163.42810.86232.2745-0.1032-1.18840.26430.6257-0.14970.31180.0294-0.40620.23160.95860.0207-0.01631.3873-0.29640.657110.300991.2894403.7505
109.6872-4.91462.60348.6757-0.62439.4059-0.1303-0.0251-0.05-0.1151-0.0725-0.01280.05390.29970.20630.7204-0.08490.01770.5939-0.0610.552719.915369.5511369.6195
111.7184-0.1551-0.84792.20280.17283.2453-0.2363-0.82451.0655-0.0087-0.32150.9411-0.7582-1.51980.43861.06760.5981-0.39142.2517-0.93651.7951-13.4942119.112395.919
122.23798.57855.9248.85925.24813.3616-1.18090.4711-1.6168-1.8680.6099-0.42970.4739-0.89170.71052.2138-0.4030.18692.1948-0.32192.3624-44.370692.1873406.7296
133.17690.989-0.78690.7870.05273.4280.0140.06160.6168-0.61550.2494-0.4566-0.69170.6588-0.26361.3797-0.09870.53460.8064-0.01151.7778-42.0911116.9717320.8955
145.9084-5.5679-0.18048.9762-0.72962.19-0.0697-0.1109-1.92540.71730.19892.34941.04390.8312-0.06521.79970.20110.05771.52760.10322.2332-12.270488.6354311.7
154.63781.1601-0.52041.51710.34674.17460.02710.10560.6852-0.01190.0434-0.2027-0.4407-0.0912-0.09591.01350.04410.12060.5470.01430.9659-71.174110.6979343.4952
164.9177-2.87953.90547.7299-0.42345.1642-0.40910.67560.32673.3830.0084-1.70650.65781.66720.48192.91030.2053-0.34413.22560.21951.7077-44.4635117.1763376.3639
173.6889-0.99760.13093.70730.60922.4593-0.34130.5957-0.3487-1.0070.1345-0.65460.4911-0.12260.20241.8567-0.13550.49470.784-0.03221.0343-64.650587.644314.6246
188.84315.75862.60768.00172.82277.6822-0.19720.2142-0.1426-0.3540.1429-0.55630.3045-0.29640.05810.96010.05760.20840.55140.08580.8074-75.871668.9726349.8814
192.78670.20331.5265.37610.63924.2390.0663-0.6939-0.65290.0830.2252-0.73650.2649-0.323-0.2270.68850.07980.02010.90250.2321.0281-73.238548.8048378.4184
206.28864.77044.00715.86691.5928.66410.2086-0.60170.5637-0.1182-0.73710.5722-0.068-0.650.51450.71650.1995-0.08980.8033-0.12330.7568-38.478841.4866355.9113
211.3947-0.36080.65184.6397-0.22273.5631-0.3296-1.24390.20872.30410.1982-0.606-0.7719-0.57720.09532.00880.2664-0.26981.4956-0.05940.9549-72.131771.8556407.9764
229.4993-6.1516-1.13266.30440.49519.3972-0.1913-0.69780.09390.43810.3698-0.1725-0.5344-0.5784-0.22450.8889-0.07950.02660.7591-0.10630.7402-77.827290.2238371.0915
232.09570.32710.89582.0351-0.25372.69850.0285-0.6933-0.60521.39020.0871-2.13110.1280.3049-0.09141.61970.1642-0.98541.47530.31332.7177-47.573143.6277405.1817
241.87431.7995-0.42672.79970.52010.35960.0063-1.14291.8253-1.15670.3268-0.5665-1.15522.333-0.36522.6837-0.44790.31843.39080.0213.5728-18.210371.2114418.2901
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resid 1:276A1 - 276
2X-RAY DIFFRACTION2chain A and resid 277:440A277 - 440
3X-RAY DIFFRACTION3chain B and resid 1:276B1 - 276
4X-RAY DIFFRACTION4chain B and resid 277:440B277 - 440
5X-RAY DIFFRACTION5chain C and resid 1:276C1 - 276
6X-RAY DIFFRACTION6chain C and resid 277:440C277 - 440
7X-RAY DIFFRACTION7chain D and resid 1:276D1 - 276
8X-RAY DIFFRACTION8chain D and resid 277:440D277 - 440
9X-RAY DIFFRACTION9chain E and resid 1:276E1 - 276
10X-RAY DIFFRACTION10chain E and resid 277:440E277 - 440
11X-RAY DIFFRACTION11chain F and resid 1:276F1 - 276
12X-RAY DIFFRACTION12chain F and resid 277:440F277 - 440
13X-RAY DIFFRACTION13chain G and resid 1:276G1 - 276
14X-RAY DIFFRACTION14chain G and resid 277:440G277 - 440
15X-RAY DIFFRACTION15chain H and resid 1:276H1 - 276
16X-RAY DIFFRACTION16chain H and resid 277:440H277 - 440
17X-RAY DIFFRACTION17chain I and resid 1:276I1 - 276
18X-RAY DIFFRACTION18chain I and resid 277:440I277 - 440
19X-RAY DIFFRACTION19chain J and resid 1:276J1 - 276
20X-RAY DIFFRACTION20chain J and resid 277:440J277 - 440
21X-RAY DIFFRACTION21chain K and resid 1:276K1 - 276
22X-RAY DIFFRACTION22chain K and resid 277:440K277 - 440
23X-RAY DIFFRACTION23chain L and resid 1:276L1 - 276
24X-RAY DIFFRACTION24chain L and resid 277:440L277 - 440

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more